*/
package jalview.gui;
+import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
+import jalview.fts.core.GFTSPanel;
+import jalview.fts.service.pdb.PDBFTSPanel;
+import jalview.fts.service.uniprot.UniprotFTSPanel;
+import jalview.io.FileFormatI;
+import jalview.io.gff.SequenceOntologyI;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
-import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.util.Platform;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.BorderLayout;
+import java.awt.Component;
import java.awt.Font;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyEvent;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import javax.swing.JButton;
import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
import javax.swing.SwingConstants;
-import javax.swing.tree.DefaultMutableTreeNode;
-public class SequenceFetcher extends JPanel implements Runnable
-{
- JLabel dbeg = new JLabel();
-
- JDatabaseTree database;
-
- JButton databaseButt;
-
- JLabel jLabel1 = new JLabel();
-
- JCheckBox replacePunctuation = new JCheckBox();
-
- JButton ok = new JButton();
+import javajs.async.AsyncSwingWorker;
- JButton clear = new JButton();
-
- JButton example = new JButton();
-
- JButton close = new JButton();
-
- JPanel jPanel1 = new JPanel();
+/**
+ * A panel where the use may choose a database source, and enter one or more
+ * accessions, to retrieve entries from the database.
+ * <p>
+ * If the selected source is Uniprot or PDB, a free text search panel is opened
+ * instead to perform the search and selection.
+ */
+@SuppressWarnings("serial")
+public class SequenceFetcher extends JPanel
+{
- JTextArea textArea = new JTextArea();
+ JLabel exampleAccession;
- JScrollPane jScrollPane1 = new JScrollPane();
+ JComboBox<String> database;
- JPanel jPanel2 = new JPanel();
+ JCheckBox replacePunctuation;
- JPanel jPanel3 = new JPanel();
+ JButton okBtn;
- JPanel jPanel4 = new JPanel();
+ JButton exampleBtn;
- BorderLayout borderLayout1 = new BorderLayout();
+ JButton closeBtn;
- BorderLayout borderLayout2 = new BorderLayout();
+ JButton backBtn;
- BorderLayout borderLayout3 = new BorderLayout();
+ JTextArea textArea;
JInternalFrame frame;
AlignFrame alignFrame;
- StringBuffer result;
+ GFTSPanel parentSearchPanel;
- final String noDbSelected = "-- Select Database --";
+ IProgressIndicator progressIndicator;
- private static jalview.ws.SequenceFetcher sfetch = null;
-
- private static long lastDasSourceRegistry = -3;
-
- private static DasSourceRegistryI dasRegistry = null;
-
- private static boolean _initingFetcher = false;
-
- private static Thread initingThread = null;
-
- int debounceTrap = 0;
+ volatile boolean _isConstructing = false;
/**
- * Blocking method that initialises and returns the shared instance of the
- * SequenceFetcher client
+ * Constructor given a client to receive any status or progress messages
+ * (currently either the Desktop, or an AlignFrame panel)
*
- * @param guiWindow
- * - where the initialisation delay message should be shown
- * @return the singleton instance of the sequence fetcher client
+ * @param guiIndic
*/
- public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
- final IProgressIndicator guiWindow)
- {
- if (_initingFetcher && initingThread != null && initingThread.isAlive())
- {
- if (guiWindow != null)
- {
- guiWindow
- .setProgressBar(
- MessageManager
- .getString("status.waiting_sequence_database_fetchers_init"),
- Thread.currentThread().hashCode());
- }
- // initting happening on another thread - so wait around to see if it
- // finishes.
- while (_initingFetcher && initingThread != null
- && initingThread.isAlive())
- {
- try
- {
- Thread.sleep(10);
- } catch (Exception e)
- {
- }
- ;
- }
- if (guiWindow != null)
- {
- guiWindow
- .setProgressBar(
- MessageManager
- .getString("status.waiting_sequence_database_fetchers_init"),
- Thread.currentThread().hashCode());
- }
- }
- if (sfetch == null
- || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
- || lastDasSourceRegistry != (jalview.bin.Cache
- .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
- .getDasSourceRegistry().getLocalSourceString())
- .hashCode())
- {
- _initingFetcher = true;
- initingThread = Thread.currentThread();
- /**
- * give a visual indication that sequence fetcher construction is occuring
- */
- if (guiWindow != null)
- {
- guiWindow.setProgressBar(MessageManager
- .getString("status.init_sequence_database_fetchers"),
- Thread.currentThread().hashCode());
- }
- dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
- dasRegistry.refreshSources();
-
- jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
- if (guiWindow != null)
- {
- guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
- }
- lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
- .getLocalSourceString()).hashCode();
- sfetch = sf;
- _initingFetcher = false;
- initingThread = null;
- }
- return sfetch;
- }
-
- private IProgressIndicator progressIndicator;
-
public SequenceFetcher(IProgressIndicator guiIndic)
{
- this.progressIndicator = guiIndic;
- final SequenceFetcher us = this;
- // launch initialiser thread
- Thread sf = new Thread(new Runnable()
- {
-
- @Override
- public void run()
- {
- if (getSequenceFetcherSingleton(progressIndicator) != null)
- {
- us.initGui(progressIndicator);
- }
- else
- {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("warn.couldnt_create_sequence_fetcher_client"),
- MessageManager
- .getString("label.couldnt_create_sequence_fetcher"),
- JOptionPane.ERROR_MESSAGE);
- }
- });
-
- // raise warning dialog
- }
- }
- });
- sf.start();
+ this(guiIndic, null, null);
}
- private class DatabaseAuthority extends DefaultMutableTreeNode
- {
-
- };
-
- private class DatabaseSource extends DefaultMutableTreeNode
- {
-
- };
-
/**
- * called by thread spawned by constructor
+ * Constructor with specified database and accession(s) to retrieve
*
- * @param guiWindow
+ * @param guiIndic
+ * @param selectedDb
+ * @param queryString
*/
- private void initGui(IProgressIndicator guiWindow)
+ public SequenceFetcher(IProgressIndicator guiIndic,
+ final String selectedDb, final String queryString)
{
- this.guiWindow = guiWindow;
- if (guiWindow instanceof AlignFrame)
- {
- alignFrame = (AlignFrame) guiWindow;
- }
- database = new JDatabaseTree(sfetch);
- try
- {
- jbInit();
- } catch (Exception ex)
+ this.progressIndicator = guiIndic;
+
+ this.guiWindow = progressIndicator;
+
+ if (progressIndicator instanceof AlignFrame)
{
- ex.printStackTrace();
+ alignFrame = (AlignFrame) progressIndicator;
}
+ jbInit(selectedDb);
+ textArea.setText(queryString);
+
frame = new JInternalFrame();
frame.setContentPane(this);
- if (new jalview.util.Platform().isAMac())
- {
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
- }
- else
- {
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
- }
+ Desktop.addInternalFrame(frame, getFrameTitle(), true, 400,
+ Platform.isAMacAndNotJS() ? 240 : 180);
}
private String getFrameTitle()
{
- return ((alignFrame == null) ? MessageManager
- .getString("label.new_sequence_fetcher") : MessageManager
- .getString("label.additional_sequence_fetcher"));
+ return ((alignFrame == null)
+ ? MessageManager.getString("label.new_sequence_fetcher")
+ : MessageManager
+ .getString("label.additional_sequence_fetcher"));
}
- private void jbInit() throws Exception
+ private void jbInit(String selectedDb)
{
- this.setLayout(borderLayout2);
+ this.setLayout(new BorderLayout());
+ database = new JComboBox<>();
database.setFont(JvSwingUtils.getLabelFont());
- dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
- jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
- jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
- jLabel1.setText(MessageManager
+ database.setPrototypeDisplayValue("ENSEMBLGENOMES ");
+ String[] sources = jalview.ws.SequenceFetcher.getInstance()
+ .getSupportedDb();
+ Arrays.sort(sources, String.CASE_INSENSITIVE_ORDER);
+ database.addItem(MessageManager.getString("action.select_ddbb"));
+ for (String source : sources)
+ {
+ database.addItem(source);
+ }
+ database.setSelectedItem(selectedDb);
+ if (database.getSelectedIndex() == -1)
+ {
+ database.setSelectedIndex(0);
+ }
+ database.setMaximumRowCount(database.getItemCount());
+ database.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ String currentSelection = (String) database.getSelectedItem();
+ updateExampleQuery(currentSelection);
+
+ if ("pdb".equalsIgnoreCase(currentSelection))
+ {
+ frame.dispose();
+ new PDBFTSPanel(SequenceFetcher.this);
+ }
+ else if ("uniprot".equalsIgnoreCase(currentSelection))
+ {
+ frame.dispose();
+ new UniprotFTSPanel(SequenceFetcher.this);
+ }
+ else
+ {
+ otherSourceAction();
+ }
+ }
+ });
+
+ exampleAccession = new JLabel("");
+ exampleAccession.setFont(new Font("Verdana", Font.BOLD, 11));
+ JLabel jLabel1 = new JLabel(MessageManager
.getString("label.separate_multiple_accession_ids"));
+ jLabel1.setFont(new Font("Verdana", Font.ITALIC, 11));
+ jLabel1.setHorizontalAlignment(SwingConstants.LEFT);
- replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
- replacePunctuation
- .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
- replacePunctuation.setText(MessageManager
- .getString("label.replace_commas_semicolons"));
- ok.setText(MessageManager.getString("action.ok"));
- ok.addActionListener(new ActionListener()
+ replacePunctuation = new JCheckBox(
+ MessageManager.getString("label.replace_commas_semicolons"));
+ replacePunctuation.setHorizontalAlignment(SwingConstants.LEFT);
+ replacePunctuation.setFont(new Font("Verdana", Font.ITALIC, 11));
+ okBtn = new JButton(MessageManager.getString("action.ok"));
+ okBtn.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
ok_actionPerformed();
}
});
- clear.setText(MessageManager.getString("action.clear"));
+ JButton clear = new JButton(MessageManager.getString("action.clear"));
clear.addActionListener(new ActionListener()
{
@Override
}
});
- example.setText(MessageManager.getString("label.example"));
- example.addActionListener(new ActionListener()
+ exampleBtn = new JButton(MessageManager.getString("label.example"));
+ exampleBtn.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
example_actionPerformed();
}
});
- close.setText(MessageManager.getString("action.close"));
- close.addActionListener(new ActionListener()
+ closeBtn = new JButton(MessageManager.getString("action.cancel"));
+ closeBtn.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
close_actionPerformed(e);
}
});
+ backBtn = new JButton(MessageManager.getString("action.back"));
+ backBtn.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ parentSearchPanel.btn_back_ActionPerformed();
+ }
+ });
+ // back not visible unless embedded
+ backBtn.setVisible(false);
+
+ textArea = new JTextArea();
textArea.setFont(JvSwingUtils.getLabelFont());
textArea.setLineWrap(true);
textArea.addKeyListener(new KeyAdapter()
}
}
});
- jPanel3.setLayout(borderLayout1);
- borderLayout1.setVgap(5);
- jPanel1.add(ok);
- jPanel1.add(example);
- jPanel1.add(clear);
- jPanel1.add(close);
- jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
- jPanel2.setLayout(borderLayout3);
- databaseButt = database.getDatabaseSelectorButton();
- databaseButt.setFont(JvSwingUtils.getLabelFont());
- database.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- debounceTrap++;
- String currentSelection = database.getSelectedItem();
- if (!currentSelection.equalsIgnoreCase("pdb"))
- {
- otherSourceAction();
- }
- if (currentSelection.equalsIgnoreCase("pdb")
- && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
- {
- pdbSourceAction();
- }
- database.action = -1;
- }
- });
- dbeg.setText("");
- jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
- jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
+ JPanel actionPanel = new JPanel();
+ actionPanel.add(backBtn);
+ actionPanel.add(exampleBtn);
+ actionPanel.add(clear);
+ actionPanel.add(okBtn);
+ actionPanel.add(closeBtn);
+
+ JPanel databasePanel = new JPanel();
+ databasePanel.setLayout(new BorderLayout());
+ databasePanel.add(database, BorderLayout.NORTH);
+ databasePanel.add(exampleAccession, BorderLayout.CENTER);
JPanel jPanel2a = new JPanel(new BorderLayout());
- jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
- jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
- jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
- // jPanel2.setPreferredSize(new Dimension())
- jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);
- this.add(jPanel3, java.awt.BorderLayout.CENTER);
- this.add(jPanel2, java.awt.BorderLayout.NORTH);
+ jPanel2a.add(jLabel1, BorderLayout.NORTH);
+ jPanel2a.add(replacePunctuation, BorderLayout.SOUTH);
+ databasePanel.add(jPanel2a, BorderLayout.SOUTH);
+
+ JPanel idsPanel = new JPanel();
+ idsPanel.setLayout(new BorderLayout(0, 5));
+ JScrollPane jScrollPane1 = new JScrollPane();
jScrollPane1.getViewport().add(textArea);
+ idsPanel.add(jScrollPane1, BorderLayout.CENTER);
+ this.add(actionPanel, BorderLayout.SOUTH);
+ this.add(idsPanel, BorderLayout.CENTER);
+ this.add(databasePanel, BorderLayout.NORTH);
}
- private void pdbSourceAction()
+ /**
+ * Answers a semi-colon-delimited string with the example query or queries for
+ * the selected database
+ *
+ * @param db
+ * @return
+ */
+ protected String getExampleQueries(String db)
{
- databaseButt.setText(database.getSelectedItem());
- new PDBSearchPanel(this);
- frame.dispose();
+ StringBuilder sb = new StringBuilder();
+ HashSet<String> hs = new HashSet<>();
+ for (DbSourceProxy dbs : jalview.ws.SequenceFetcher.getInstance()
+ .getSourceProxy(db))
+ {
+ String tq = dbs.getTestQuery();
+ if (hs.add(tq)) // not a duplicate source
+ {
+ if (sb.length() > 0)
+ {
+ sb.append(";");
+ }
+ sb.append(tq);
+ }
+ }
+ return sb.toString();
}
- private void otherSourceAction()
+ /**
+ * Action on selecting a database other than Uniprot or PDB is to enable or
+ * disable 'Replace commas', and await input in the query field
+ */
+ protected void otherSourceAction()
{
try
{
- databaseButt.setText(database.getSelectedItem()
- + (database.getSelectedSources().size() > 1 ? " (and "
- + database.getSelectedSources().size() + " others)"
- : ""));
- String eq = database.getExampleQueries();
- dbeg.setText(MessageManager.formatMessage(
- "label.example_query_param", new String[] { eq }));
+ String eq = exampleAccession.getText();
+ // TODO this should be a property of the SequenceFetcher whether commas
+ // are allowed in the IDs...
+
boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
- for (DbSourceProxy dbs : database.getSelectedSources())
- {
- if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
- {
- enablePunct = false;
- break;
- }
- }
replacePunctuation.setEnabled(enablePunct);
} catch (Exception ex)
{
- dbeg.setText("");
+ exampleAccession.setText("");
replacePunctuation.setEnabled(true);
}
- jPanel2.repaint();
+ repaint();
}
+ /**
+ * Sets the text of the example query to incorporate the example accession
+ * provided by the selected database source
+ *
+ * @param selectedDatabase
+ * @return
+ */
+ protected String updateExampleQuery(String selectedDatabase)
+ {
+ String eq = getExampleQueries(selectedDatabase);
+ exampleAccession.setText(MessageManager
+ .formatMessage("label.example_query_param", new String[]
+ { eq }));
+ return eq;
+ }
+
+ /**
+ * Action on clicking the 'Example' button is to write the example accession
+ * as the query text field value
+ */
protected void example_actionPerformed()
{
- DbSourceProxy db = null;
- try
- {
- textArea.setText(database.getExampleQueries());
- } catch (Exception ex)
- {
- }
- jPanel3.repaint();
+ String eq = getExampleQueries((String) database.getSelectedItem());
+ textArea.setText(eq);
+ repaint();
}
+ /**
+ * Clears the query input field
+ */
protected void clear_actionPerformed()
{
textArea.setText("");
- jPanel3.repaint();
+ repaint();
}
- public void close_actionPerformed(ActionEvent e)
+ /**
+ * Action on Close button is to close this frame, and also (if it is embedded
+ * in a search panel) to close the search panel
+ *
+ * @param e
+ */
+ protected void close_actionPerformed(ActionEvent e)
{
try
{
frame.setClosed(true);
+ if (parentSearchPanel != null)
+ {
+ parentSearchPanel.btn_cancel_ActionPerformed();
+ }
} catch (Exception ex)
{
}
}
+ /**
+ * Action on OK is to start the fetch for entered accession(s)
+ */
public void ok_actionPerformed()
{
- databaseButt.setEnabled(false);
- example.setEnabled(false);
+ /*
+ * tidy inputs and check there is something to search for
+ */
+ String t0 = textArea.getText();
+ String text = t0.trim();
+ if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
+ {
+ text = text.replace(",", ";");
+ }
+ text = text.replaceAll("(\\s|[; ])+", ";");
+ if (!t0.equals(text))
+ {
+ textArea.setText(text);
+ }
+ if (text.isEmpty())
+ {
+ // todo i18n
+ showErrorMessage(
+ "Please enter a (semi-colon separated list of) database id(s)");
+ resetDialog();
+ return;
+ }
+ exampleBtn.setEnabled(false);
textArea.setEnabled(false);
- ok.setEnabled(false);
- close.setEnabled(false);
-
- Thread worker = new Thread(this);
- worker.start();
- }
-
- private void resetDialog()
- {
- databaseButt.setEnabled(true);
- example.setEnabled(true);
- textArea.setEnabled(true);
- ok.setEnabled(true);
- close.setEnabled(true);
+ okBtn.setEnabled(false);
+ closeBtn.setEnabled(false);
+ backBtn.setEnabled(false);
+ fetch(null, true);
}
- @Override
- public void run()
+ public void fetch(String ids, boolean isAsync)
{
- String error = "";
- if (!database.hasSelection())
+ isAsync &= Platform.isJS();
+ if (ids == null)
{
- error += "Please select the source database\n";
- }
- // TODO: make this transformation more configurable
- com.stevesoft.pat.Regex empty;
- if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
- {
- empty = new com.stevesoft.pat.Regex(
- // replace commas and spaces with a semicolon
- "(\\s|[,; ])+", ";");
+ ids = textArea.getText();
}
else
{
- // just turn spaces and semicolons into single semicolons
- empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
+ textArea.setText(ids);
}
- textArea.setText(empty.replaceAll(textArea.getText()));
- // see if there's anthing to search with
- if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
- .getText()))
+ Component parent = null; // or this
+ String title = null; // or some title for the progress monitor
+ int min = AsyncFetchTask.STATE_INIT;
+ int max = AsyncFetchTask.STATE_DONE;
+ int msDelay = (isAsync ? 5 : 0);
+ new AsyncFetchTask(ids, parent, title, msDelay, min, max).execute();
+ }
+
+
+ protected void resetDialog()
+ {
+ exampleBtn.setEnabled(true);
+ textArea.setEnabled(true);
+ okBtn.setEnabled(true);
+ closeBtn.setEnabled(true);
+ backBtn.setEnabled(parentSearchPanel != null);
+ }
+
+ /**
+ * This asynchronous class allows for a single-threaded state machine
+ * SwingWorker to process a list of requests from multiple sources.
+ *
+ * A standard ProcessMonitor could be attached to this task, but it is
+ * currently not.
+ *
+ * @author hansonr
+ *
+ */
+ private class AsyncFetchTask extends AsyncSwingWorker
+ {
+
+ private boolean addToLast = false;
+
+ private List<String> aresultq = new ArrayList<>();
+
+ private List<String> presultTitle = new ArrayList<>();
+
+ private List<AlignmentI> presult = new ArrayList<>();
+
+ private List<AlignmentI> aresult = new ArrayList<>();
+
+ private FeatureSettingsModelI preferredFeatureColours = null;
+
+ private List<DbSourceProxy> sources;
+
+ private Iterator<DbSourceProxy> sourceIterator;
+
+ private String[] fetchArray;
+
+ private List<String> fetchList;
+
+ private Iterator<String> fetchIterator;
+
+ private int fetchCount;
+
+ private DbSourceProxy source;
+
+ private String ids;
+
+ public AsyncFetchTask(String ids, Component owner, String title,
+ int delayMillis,
+ int min, int max)
{
- error += "Please enter a (semi-colon separated list of) database id(s)";
+ super(owner, title, delayMillis, min, max);
+ this.ids = ids;
}
- if (error.length() > 0)
+
+ @Override
+ public void initAsync()
{
- showErrorMessage(error);
- resetDialog();
- return;
+ sources = jalview.ws.SequenceFetcher.getInstance()
+ .getSourceProxy((String) database.getSelectedItem());
+ sourceIterator = sources.iterator();
+ fetchArray = ids.trim().split(";");
+ fetchList = Arrays.asList(fetchArray);
}
- // TODO: Refactor to GUI independent code and write tests.
- // indicate if successive sources should be merged into one alignment.
- boolean addToLast = false;
- ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
- ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
- Iterator<DbSourceProxy> proxies = database.getSelectedSources()
- .iterator();
- String[] qries;
- List<String> nextfetch = Arrays.asList(qries = textArea.getText()
- .split(";"));
- Iterator<String> en = Arrays.asList(new String[0]).iterator();
- int nqueries = qries.length;
- while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
- {
- if (!en.hasNext() && nextfetch.size() > 0)
- {
- en = nextfetch.iterator();
- nqueries = nextfetch.size();
- // save the remaining queries in the original array
- qries = nextfetch.toArray(new String[nqueries]);
- nextfetch = new ArrayList<String>();
- }
- DbSourceProxy proxy = proxies.next();
- boolean isAliSource = false;
- try
+ private final static int STATE_INIT = 0;
+
+ private final static int STATE_NEXT_SOURCE = 10;
+
+ private final static int STATE_FETCH_SINGLE = 30;
+
+ private final static int STATE_FETCH_MULTIPLE = 40;
+
+ private final static int STATE_PROCESS = 50;
+
+ private final static int STATE_PARSE_RESULTS = 80;
+
+ private final static int STATE_DONE = 100;
+
+ @Override
+ public int doInBackgroundAsync(int progress)
+ {
+ switch (progress)
{
- // update status
- guiWindow
- .setProgressBar(MessageManager.formatMessage(
- "status.fetching_sequence_queries_from",
- new String[] {
- Integer.valueOf(nqueries).toString(),
- proxy.getDbName() }), Thread.currentThread()
- .hashCode());
- isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
- if (proxy.getAccessionSeparator() == null)
+ case STATE_INIT:
+ case STATE_NEXT_SOURCE:
+ boolean doneFetching = (fetchIterator == null
+ || !fetchIterator.hasNext());
+ boolean havePending = (fetchList.size() > 0);
+ if (!sourceIterator.hasNext() || doneFetching && !havePending)
+ {
+ showProgress((presult.size() > 0)
+ ? MessageManager.getString("status.parsing_results")
+ : MessageManager.getString("status.processing"));
+ return STATE_PARSE_RESULTS;
+ }
+ source = sourceIterator.next();
+ if (doneFetching)
+ {
+ // if we are here, we must have some pending still
+ fetchCount = fetchList.size();
+ fetchIterator = fetchList.iterator();
+ // save the remaining queries in the original array
+ fetchArray = fetchList.toArray(new String[fetchCount]);
+ // and clear the
+ fetchList = new ArrayList<>();
+ }
+ showProgress(MessageManager.formatMessage(
+ "status.fetching_sequence_queries_from", new String[]
+ { Integer.valueOf(fetchCount).toString(),
+ source.getDbName() }));
+ return (source.getMaximumQueryCount() == 1 ? STATE_FETCH_SINGLE
+ : STATE_FETCH_MULTIPLE);
+ case STATE_FETCH_SINGLE:
+ if (fetchIterator.hasNext())
{
- while (en.hasNext())
+ // source only handles one accession id at a time
+ try
{
- String item = en.next();
- try
+ if (delayMillis == 0)
{
- if (aresult != null)
- {
- try
- {
- // give the server a chance to breathe
- Thread.sleep(5);
- } catch (Exception e)
- {
- //
- }
-
- }
-
- AlignmentI indres = null;
- try
- {
- indres = proxy.getSequenceRecords(item);
- } catch (OutOfMemoryError oome)
- {
- new OOMWarning("fetching " + item + " from "
- + proxy.getDbName(), oome, this);
- }
- if (indres != null)
- {
- aresultq.add(item);
- aresult.add(indres);
- }
- else
- {
- nextfetch.add(item);
- }
- } catch (Exception e)
+ // for CrossRef2xmlTest only
+ Thread.sleep(5);
+ }
+ String accession = fetchIterator.next();
+ if (!fetchSingleAccession(source, accession, aresultq, aresult))
+ {
+ fetchList.add(accession);
+ }
+ } catch (Throwable e)
+ {
+ if (!showError(e))
{
- jalview.bin.Cache.log.info("Error retrieving " + item
- + " from " + proxy.getDbName(), e);
- nextfetch.add(item);
+ return STATE_DONE;
}
}
+ return STATE_FETCH_SINGLE;
}
- else
+ return STATE_PROCESS;
+ case STATE_FETCH_MULTIPLE:
+ // proxy can fetch multiple accessions at one time
+ try
+ {
+ fetchMultipleAccessions(source, fetchIterator, aresultq, aresult,
+ fetchList);
+ } catch (Throwable e)
{
- StringBuffer multiacc = new StringBuffer();
- ArrayList<String> tosend = new ArrayList<String>();
- while (en.hasNext())
+ if (!showError(e))
{
- String nel = en.next();
- tosend.add(nel);
- multiacc.append(nel);
- if (en.hasNext())
+ return STATE_DONE;
+ }
+ }
+ return STATE_PROCESS;
+ case STATE_PROCESS:
+ // Stack results ready for opening in alignment windows
+ if (aresult != null && aresult.size() > 0)
+ {
+ FeatureSettingsModelI proxyColourScheme = source
+ .getFeatureColourScheme();
+ if (proxyColourScheme != null)
+ {
+ preferredFeatureColours = proxyColourScheme;
+ }
+
+ AlignmentI ar = null;
+ if (source.isAlignmentSource())
+ {
+ addToLast = false;
+ // new window for each result
+ while (aresult.size() > 0)
{
- multiacc.append(proxy.getAccessionSeparator());
+ presult.add(aresult.remove(0));
+ presultTitle.add(aresultq.remove(0) + " "
+ + getDefaultRetrievalTitle());
}
}
- try
+ else
{
- AlignmentI rslt;
- SequenceI[] rs;
- List<String> nores = new ArrayList<String>();
- rslt = proxy.getSequenceRecords(multiacc.toString());
- if (rslt == null || rslt.getHeight() == 0)
+ String titl = null;
+ if (addToLast && presult.size() > 0)
{
- // no results - pass on all queries to next source
- nextfetch.addAll(tosend);
+ ar = presult.remove(presult.size() - 1);
+ titl = presultTitle.remove(presultTitle.size() - 1);
}
- else
+ // concatenate all results in one window
+ while (aresult.size() > 0)
{
- aresultq.add(multiacc.toString());
- aresult.add(rslt);
-
- rs = rslt.getSequencesArray();
- // search for each query in the dbrefs associated with each
- // sequence
- // returned.
- // ones we do not find will be used to query next source (if any)
- for (String q : tosend)
+ if (ar == null)
{
- DBRefEntry dbr = new DBRefEntry(), found[] = null;
- dbr.setSource(proxy.getDbSource());
- dbr.setVersion(null);
- String accId = DBRefUtils.processQueryToAccessionFor(proxy,
- q);
- dbr.setAccessionId(accId);
- boolean rfound = false;
- for (int r = 0; r < rs.length; r++)
- {
- if (rs[r] != null
- && (found = DBRefUtils.searchRefs(
- rs[r].getDBRef(), dbr)) != null
- && found.length > 0)
- {
- rfound = true;
- rs[r] = null;
- continue;
- }
- }
- if (!rfound)
- {
- nextfetch.add(q);
- }
+ ar = aresult.remove(0);
+ }
+ else
+ {
+ ar.append(aresult.remove(0));
}
}
- } catch (OutOfMemoryError oome)
+ addToLast = true;
+ presult.add(ar);
+ presultTitle.add(titl);
+ }
+ }
+ showProgress(MessageManager.getString("status.finshed_querying"));
+ return STATE_NEXT_SOURCE;
+ case STATE_PARSE_RESULTS:
+ while (presult.size() > 0)
+ {
+ parseResult(presult.remove(0), presultTitle.remove(0), null,
+ preferredFeatureColours);
+ }
+ break;
+ }
+ return STATE_DONE;
+ }
+
+ private void showProgress(String msg)
+ {
+ guiWindow.setProgressBar(msg, Thread.currentThread().hashCode());
+ }
+
+ @Override
+ public void doneAsync()
+ {
+ showProgress(null);
+ if (fetchList.size() > 0)
+ {
+ StringBuffer sb = new StringBuffer();
+ sb.append("Didn't retrieve the following "
+ + (fetchList.size() == 1 ? "query"
+ : fetchList.size() + " queries")
+ + ": \n");
+ int l = sb.length(), lr = 0;
+ for (String s : fetchList)
+ {
+ if (l != sb.length())
+ {
+ sb.append("; ");
+ }
+ if (lr - sb.length() > 40)
{
- new OOMWarning("fetching " + multiacc + " from "
- + database.getSelectedItem(), oome, this);
+ sb.append("\n");
}
+ sb.append(s);
}
+ showErrorMessage(sb.toString());
+ }
+ resetDialog();
+ }
- } catch (Exception e)
+ private boolean showError(Throwable e)
+ {
+ String problem = "retrieving " + ids + " from "
+ + database.getSelectedItem();
+ if (e instanceof Exception)
{
- showErrorMessage("Error retrieving " + textArea.getText()
- + " from " + database.getSelectedItem());
- // error
- // +="Couldn't retrieve sequences from "+database.getSelectedItem();
+ showErrorMessage("Error " + problem);
System.err.println("Retrieval failed for source ='"
+ database.getSelectedItem() + "' and query\n'"
- + textArea.getText() + "'\n");
- e.printStackTrace();
- } catch (OutOfMemoryError e)
+ + ids + "'\n");
+ }
+ else if (e instanceof OutOfMemoryError)
{
- // resets dialog box - so we don't use OOMwarning here.
- showErrorMessage("Out of Memory when retrieving "
- + textArea.getText()
- + " from "
- + database.getSelectedItem()
+ showErrorMessage("Out of Memory when " + problem
+ "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
- e.printStackTrace();
- } catch (Error e)
- {
- showErrorMessage("Serious Error retrieving " + textArea.getText()
- + " from " + database.getSelectedItem());
- e.printStackTrace();
+ // option here to return false and quit this, but that is not how
+ // original code works - BH
+ // return false;
}
- // Stack results ready for opening in alignment windows
- if (aresult != null && aresult.size() > 0)
+ else
{
- AlignmentI ar = null;
- if (isAliSource)
- {
- addToLast = false;
- // new window for each result
- while (aresult.size() > 0)
- {
- presult.add(aresult.remove(0));
- presultTitle.add(aresultq.remove(0) + " "
- + getDefaultRetrievalTitle());
- }
- }
- else
- {
- String titl = null;
- if (addToLast && presult.size() > 0)
- {
- ar = presult.remove(presult.size() - 1);
- titl = presultTitle.remove(presultTitle.size() - 1);
- }
- // concatenate all results in one window
- while (aresult.size() > 0)
- {
- if (ar == null)
- {
- ar = aresult.remove(0);
- }
- else
- {
- ar.append(aresult.remove(0));
- }
- ;
- }
- addToLast = true;
- presult.add(ar);
- presultTitle.add(titl);
- }
+ showErrorMessage("Serious Error " + problem);
}
- guiWindow.setProgressBar(MessageManager
- .getString("status.finshed_querying"), Thread.currentThread()
- .hashCode());
+ e.printStackTrace();
+ return true;
}
- guiWindow.setProgressBar(
- (presult.size() > 0) ? MessageManager
- .getString("status.parsing_results") : MessageManager
- .getString("status.processing"), Thread.currentThread()
- .hashCode());
- // process results
- while (presult.size() > 0)
- {
- parseResult(presult.remove(0), presultTitle.remove(0), null);
+
+ }
+
+ /**
+ * Tries to fetch one or more accession ids from the database proxy
+ *
+ * @param proxy
+ * @param accessions
+ * the queries to fetch
+ * @param aresultq
+ * a successful queries list to add to
+ * @param aresult
+ * a list of retrieved alignments to add to
+ * @param nextFetch
+ * failed queries are added to this list
+ * @throws Exception
+ */
+ void fetchMultipleAccessions(DbSourceProxy proxy,
+ Iterator<String> accessions, List<String> aresultq,
+ List<AlignmentI> aresult, List<String> nextFetch) throws Exception
+ {
+ StringBuilder multiacc = new StringBuilder();
+ List<String> tosend = new ArrayList<>();
+ while (accessions.hasNext())
+ {
+ String nel = accessions.next();
+ tosend.add(nel);
+ multiacc.append(nel);
+ if (accessions.hasNext())
+ {
+ multiacc.append(proxy.getAccessionSeparator());
+ }
}
- // only remove visual delay after we finished parsing.
- guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
- if (nextfetch.size() > 0)
- {
- StringBuffer sb = new StringBuffer();
- sb.append("Didn't retrieve the following "
- + (nextfetch.size() == 1 ? "query" : nextfetch.size()
- + " queries") + ": \n");
- int l = sb.length(), lr = 0;
- for (String s : nextfetch)
+
+ try
+ {
+ String query = multiacc.toString();
+ AlignmentI rslt = proxy.getSequenceRecords(query);
+ if (rslt == null || rslt.getHeight() == 0)
{
- if (l != sb.length())
- {
- sb.append("; ");
- }
- if (lr - sb.length() > 40)
+ // no results - pass on all queries to next source
+ nextFetch.addAll(tosend);
+ }
+ else
+ {
+ aresultq.add(query);
+ aresult.add(rslt);
+ if (tosend.size() > 1)
{
- sb.append("\n");
+ checkResultForQueries(rslt, tosend, nextFetch, proxy);
}
- sb.append(s);
}
- showErrorMessage(sb.toString());
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning("fetching " + multiacc + " from "
+ + database.getSelectedItem(), oome, this);
}
- resetDialog();
}
- AlignmentI parseResult(String result, String title)
+ /**
+ * Query for a single accession id via the database proxy
+ *
+ * @param proxy
+ * @param accession
+ * @param aresultq
+ * a list of successful queries to add to
+ * @param aresult
+ * a list of retrieved alignments to add to
+ * @return true if the fetch was successful, else false
+ */
+ boolean fetchSingleAccession(DbSourceProxy proxy, String accession,
+ List<String> aresultq, List<AlignmentI> aresult)
{
- String format = new IdentifyFile().identify(result, "Paste");
- AlignmentI sequences = null;
- if (FormatAdapter.isValidFormat(format))
+ boolean success = false;
+ try
{
- sequences = null;
+ // BH no longer necessary; we are doing 5-ms asynchronous delays all along
+ // if (aresult != null)
+ // {
+ // try
+ // {
+ // // give the server a chance to breathe
+ // Thread.sleep(5);
+ // } catch (Exception e)
+ // {
+ // //
+ // }
+ // }
+ //
+ AlignmentI indres = null;
try
{
- sequences = new FormatAdapter().readFile(result.toString(),
- "Paste", format);
- } catch (Exception ex)
+ indres = proxy.getSequenceRecords(accession);
+ } catch (OutOfMemoryError oome)
{
+ new OOMWarning(
+ "fetching " + accession + " from " + proxy.getDbName(),
+ oome, this);
}
-
- if (sequences != null)
+ if (indres != null)
{
- return parseResult(sequences, title, format);
+ aresultq.add(accession);
+ aresult.add(indres);
+ success = true;
}
- }
- else
+ } catch (Exception e)
{
- showErrorMessage("Error retrieving " + textArea.getText() + " from "
- + database.getSelectedItem());
+ Cache.log.info("Error retrieving " + accession + " from "
+ + proxy.getDbName(), e);
}
+ return success;
+ }
- return null;
+ /**
+ * Checks which of the queries were successfully retrieved by searching the
+ * DBRefs of the retrieved sequences for a match. Any not found are added to
+ * the 'nextFetch' list.
+ *
+ * @param rslt
+ * @param queries
+ * @param nextFetch
+ * @param proxy
+ */
+ void checkResultForQueries(AlignmentI rslt, List<String> queries,
+ List<String> nextFetch, DbSourceProxy proxy)
+ {
+ SequenceI[] rs = rslt.getSequencesArray();
+
+ for (String q : queries)
+ {
+ // BH 2019.01.25 dbr is never used.
+ // DBRefEntry dbr = new DBRefEntry();
+ // dbr.setSource(proxy.getDbSource());
+ // dbr.setVersion(null);
+ String accId = proxy.getAccessionIdFromQuery(q);
+ // dbr.setAccessionId(accId);
+ boolean rfound = false;
+ for (int r = 0, nr = rs.length; r < nr; r++)
+ {
+ if (rs[r] != null)
+ {
+ List<DBRefEntry> found = DBRefUtils.searchRefs(rs[r].getDBRefs(),
+ accId);
+ if (!found.isEmpty())
+ {
+ rfound = true;
+ break;
+ }
+ }
+ }
+ if (!rfound)
+ {
+ nextFetch.add(q);
+ }
+ }
}
/**
}
AlignmentI parseResult(AlignmentI al, String title,
- String currentFileFormat)
+ FileFormatI currentFileFormat,
+ FeatureSettingsModelI preferredFeatureColours)
{
if (al != null && al.getHeight() > 0)
AlignFrame.DEFAULT_HEIGHT);
if (currentFileFormat != null)
{
- af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
- // FORMAT FOR
- // NON-FormatAdapter Sourced
- // Alignments?
+ af.currentFileFormat = currentFileFormat;
}
- SequenceFeature[] sfs = null;
- List<SequenceI> alsqs;
- synchronized (alsqs = al.getSequences())
+ List<SequenceI> alsqs = al.getSequences();
+ synchronized (alsqs)
{
for (SequenceI sq : alsqs)
{
- if ((sfs = sq.getSequenceFeatures()) != null)
+ if (sq.getFeatures().hasFeatures())
{
- if (sfs.length > 0)
- {
- af.setShowSeqFeatures(true);
- break;
- }
+ af.setShowSeqFeatures(true);
+ break;
}
-
}
}
+
+ if (preferredFeatureColours != null)
+ {
+ af.getViewport().applyFeaturesStyle(preferredFeatureColours);
+ }
+ if (Cache.getDefault(Preferences.HIDE_INTRONS, true))
+ {
+ af.hideFeatureColumns(SequenceOntologyI.EXON, false);
+ }
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- af.statusBar.setText(MessageManager
+ af.setStatus(MessageManager
.getString("label.successfully_pasted_alignment_file"));
try
{
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
- false));
+ af.setMaximum(
+ Cache.getDefault(Preferences.SHOW_FULLSCREEN, false));
} catch (Exception ex)
{
}
@Override
public void run()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+ error,
MessageManager.getString("label.error_retrieving_data"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
{
this.progressIndicator = progressIndicator;
}
+
+ /**
+ * Hide this panel (on clicking the database button to open the database
+ * chooser)
+ */
+ void hidePanel()
+ {
+ frame.setVisible(false);
+ }
+
+ /**
+ * Called to modify the search panel for embedding as an alternative tab of a
+ * free text search panel. The database choice list is hidden (since the
+ * choice has been made), and a Back button is made visible (which reopens the
+ * Sequence Fetcher panel).
+ *
+ * @param parentPanel
+ */
+ public void embedIn(GFTSPanel parentPanel)
+ {
+ database.setVisible(false);
+ backBtn.setVisible(true);
+ parentSearchPanel = parentPanel;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff